Rolf Backofen

ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 50

Top Venues

RNA biology

GigaScience

Nature communications

Nucleic acids research

Albert-Ludwigs-Universität Freiburg Institut für Informatik

This page only lists publications with an associated author ORCID identifier.

Affiliation History

Albert-Ludwigs-Universität Freiburg Institut für Informatik Jul 01 2005

Germany

Full Professor :: Chair for Bioinformatics

Friedrich Schiller Universität Jena Institut für Informatik Oct 01 2001

Germany

Full Professor :: Chair for Bioinformatics

Ludwig-Maximilians-Universität München Feb 01 1996 - Oct 01 2001

Germany

Postdoc :: Computer Science

Deutsches Forschungszentrum für Künstliche Intelligenz GmbH Apr 01 1990 - Mar 31 1996

Germany

Researcher Fellow

Publications

Teresa Müller, Stefan Mautner, Pavankumar Videm, Florian Eggenhofer, Martin Raden, Rolf Backofen
CheRRI-Accurate classification of the biological relevance of putative RNA-RNA interaction sites. GigaScience 13 (2024)
Ute A Hoffmann, Elisabeth Lichtenberg, Said N Rogh, Raphael Bilger, Viktoria Reimann, Florian Heyl, Rolf Backofen, Claudia Steglich, Wolfgang R Hess, Annegret Wilde
The role of the 5' sensing function of ribonuclease E in cyanobacteria. RNA biology 21 (1) (2024)
Ute A Hoffmann, Elisabeth Lichtenberg, Said N Rogh, Raphael Bilger, Viktoria Reimann, Florian Heyl, Rolf Backofen, Claudia Steglich, Wolfgang R Hess, Annegret Wilde
The role of the 5' sensing function of ribonuclease E in cyanobacteria. RNA biology 21 (1) (2024)
Ute A Hoffmann, Elisabeth Lichtenberg, Said N Rogh, Raphael Bilger, Viktoria Reimann, Florian Heyl, Rolf Backofen, Claudia Steglich, Wolfgang R Hess, Annegret Wilde
The role of the 5' sensing function of ribonuclease E in cyanobacteria. RNA biology 21 (1) (2024)
Teresa Müller, Stefan Mautner, Pavankumar Videm, Florian Eggenhofer, Martin Raden, Rolf Backofen
CheRRI-Accurate classification of the biological relevance of putative RNA-RNA interaction sites. GigaScience 13 (2024)
Frederic Runge, Jörg Franke, Daniel Fertmann, Rolf Backofen, Frank Hutter
Partial RNA design. Bioinformatics (Oxford, England) 40 (Supplement_1) (2024)
Veerendra P Gadekar, Alexander Welford Munk, Milad Miladi, Alexander Junge, Rolf Backofen, Stefan Ernst Seemann, Jan Gorodkin
Clusters of mammalian conserved RNA structures in UTRs associate with RBP binding sites. NAR genomics and bioinformatics 6 (3) (2024)
Frederic Runge, Jörg Franke, Daniel Fertmann, Rolf Backofen, Frank Hutter
Partial RNA design. Bioinformatics (Oxford, England) 40 (Supplement_1) (2024)
Teresa Müller, Stefan Mautner, Pavankumar Videm, Florian Eggenhofer, Martin Raden, Rolf Backofen
CheRRI-Accurate classification of the biological relevance of putative RNA-RNA interaction sites. GigaScience 13 (2024)
Ute A Hoffmann, Elisabeth Lichtenberg, Said N Rogh, Raphael Bilger, Viktoria Reimann, Florian Heyl, Rolf Backofen, Claudia Steglich, Wolfgang R Hess, Annegret Wilde
The role of the 5' sensing function of ribonuclease E in cyanobacteria. RNA biology 21 (1) (2024)
Veerendra P Gadekar, Alexander Welford Munk, Milad Miladi, Alexander Junge, Rolf Backofen, Stefan Ernst Seemann, Jan Gorodkin
Clusters of mammalian conserved RNA structures in UTRs associate with RBP binding sites. NAR genomics and bioinformatics 6 (3) (2024)
Frederic Runge, Jörg Franke, Daniel Fertmann, Rolf Backofen, Frank Hutter
Partial RNA design. Bioinformatics (Oxford, England) 40 (Supplement_1) (2024)
Axel Fehrenbach, Alexander Mitrofanov, Omer S Alkhnbashi, Rolf Backofen, Franz Baumdicker
SpacerPlacer: ancestral reconstruction of CRISPR arrays reveals the evolutionary dynamics of spacer deletions. Nucleic acids research (2024)
Sabine Steffens, Katrin Schroder, Martina Krüger, Christoph Maack, Katrin Streckfuß-Bömeke, Johannes Backs, Rolf Backofen, Bettina Baeßler, Yvan Devaux, Ralf Gilsbach, Jordi Heijman, Jochen Knaus, Rafael Kramann, Dominik K Linz, Allyson L Lister, Henrike Maatz, Lars Maegdefessel, Manuel Mayr, Benjamin Meder, Sara Yasemin Nussbeck, Eva A Rog-Zielinska, Marcel H Schulz, Albert Sickmann, Gökhan Yigit, Peter Kohl
The challenges of research data management in cardiovascular science: a DGK and DZHK position paper-executive summary. Clinical research in cardiology : official journal of the German Cardiac Society (2023)
Franziska Wimmer, Frank Englert, Katharina G Wandera, Omer S Alkhnbashi, Scott P Collins, Rolf Backofen, Chase L Beisel
Interrogating two extensively self-targeting Type I CRISPR-Cas systems in Xanthomonas albilineans reveals distinct anti-CRISPR proteins that block DNA degradation. Nucleic acids research (2023)
Emilia Neuwirt, Giovanni Magnani, Tamara Ćiković, Svenja Wöhrle, Larissa Fischer, Anna Kostina, Stephan Flemming, Nora J Fischenich, Benedikt S Saller, Oliver Gorka, Steffen Renner, Claudia Agarinis, Christian N Parker, Andreas Boettcher, Christopher J Farady, Rebecca Kesselring, Christopher Berlin, Rolf Backofen, Marta Rodriguez-Franco, Clemens Kreutz, Marco Prinz, Martina Tholen, Thomas Reinheckel, Thomas Ott, Christina J Groß, Philipp J Jost, Olaf Gross
Tyrosine kinase inhibitors can activate the NLRP3 inflammasome in myeloid cells through lysosomal damage and cell lysis. Science signaling 16 (768) (2023)
Sandra Fischer, Chiara Lichtenthaeler, Anastasiya Stepanenko, Florian Heyl, Daniel Maticzka, Katrin Kemmerer, Melina Klostermann, Rolf Backofen, Kathi Zarnack, Julia E Weigand
Heterogenous nuclear ribonucleoprotein D-like controls endothelial cell functions. Biological chemistry (2023)
Anup Kumar, Gianmauro Cuccuru, Bjoern Andreas Gruening, Rolf Backofen
An accessible infrastructure for artificial intelligence using a Docker-based JupyterLab in Galaxy. GigaScience 12 (2023)
Lydia Hadjeras, Benjamin Heiniger, Sandra Maaß, Robina Scheuer, Rick Gelhausen, Saina Azarderakhsh, Susanne Barth-Weber, Rolf Backofen, Dörte Becher, Christian H Ahrens, Cynthia Mira Sharma, Elena Evguenieva-Hackenberg
Unraveling the small proteome of the plant symbiont Sinorhizobium meliloti by ribosome profiling and proteogenomics. microLife 4 (2023)
Lydia Hadjeras, Jürgen Bartel, Lisa-Katharina Maier, Sandra Maaß, Verena Vogel, Sarah L Svensson, Florian Eggenhofer, Rick Gelhausen, Teresa Müller, Omer S Alkhnbashi, Rolf Backofen, Dörte Becher, Cynthia Mira Sharma, Anita Marchfelder
Revealing the small proteome of Haloferax volcanii by combining ribosome profiling and small-protein optimized mass spectrometry. microLife 4 (2023)
Emilia Neuwirt, Giovanni Magnani, Tamara Ćiković, Svenja Wöhrle, Larissa Fischer, Anna Kostina, Stephan Flemming, Nora J Fischenich, Benedikt S Saller, Oliver Gorka, Steffen Renner, Claudia Agarinis, Christian N Parker, Andreas Boettcher, Christopher J Farady, Rebecca Kesselring, Christopher Berlin, Rolf Backofen, Marta Rodriguez-Franco, Clemens Kreutz, Marco Prinz, Martina Tholen, Thomas Reinheckel, Thomas Ott, Christina J Groß, Philipp J Jost, Olaf Gross
Tyrosine kinase inhibitors can activate the NLRP3 inflammasome in myeloid cells through lysosomal damage and cell lysis. Science signaling 16 (768) (2023)
Anup Kumar, Gianmauro Cuccuru, Bjoern Andreas Gruening, Rolf Backofen
An accessible infrastructure for artificial intelligence using a Docker-based JupyterLab in Galaxy. GigaScience 12 (2023)
Thomas Schwarzl, Sudeep Sahadevan, Benjamin Lang, Milad Miladi, Rolf Backofen, Wolfgang Huber, Matthias W Hentze, Gian Gaetano Tartaglia
Improved discovery of RNA-binding protein binding sites in eCLIP data using DEWSeq. Nucleic acids research (2023)
Emilia Neuwirt, Giovanni Magnani, Tamara Ćiković, Svenja Wöhrle, Larissa Fischer, Anna Kostina, Stephan Flemming, Nora J Fischenich, Benedikt S Saller, Oliver Gorka, Steffen Renner, Claudia Agarinis, Christian N Parker, Andreas Boettcher, Christopher J Farady, Rebecca Kesselring, Christopher Berlin, Rolf Backofen, Marta Rodriguez-Franco, Clemens Kreutz, Marco Prinz, Martina Tholen, Thomas Reinheckel, Thomas Ott, Christina J Groß, Philipp J Jost, Olaf Gross
Tyrosine kinase inhibitors can activate the NLRP3 inflammasome in myeloid cells through lysosomal damage and cell lysis. Science signaling 16 (768) (2023)
Florian Heyl, Rolf Backofen
StoatyDive: Evaluation and classification of peak profiles for sequencing data. GigaScience 10 (6) (2022)
Alexander Mitrofanov, Marcus Ziemann, Omer S Alkhnbashi, Wolfgang R Hess, Rolf Backofen
CRISPRtracrRNA: robust approach for CRISPR tracrRNA detection. Bioinformatics (Oxford, England) 38 (Supplement_2) (2022)
Chunyu Liao, Sahil Sharma, Sarah L Svensson, Anuja Kibe, Zasha Weinberg, Omer S Alkhnbashi, Thorsten Bischler, Rolf Backofen, Neva Caliskan, Cynthia Mira Sharma, Chase L Beisel
Spacer prioritization in CRISPR-Cas9 immunity is enabled by the leader RNA. Nature microbiology 7 (4) (2022)
Omar Mossad, Bérénice Batut, Bahtiyar Yilmaz, Nikolaos Dokalis, Charlotte Mezö, Elisa Nent, Lara Susann Nabavi, Melanie Mayer, Feres José Mocayar Maron, Joerg M Buescher, Mercedes Gomez de Agüero, Antal Szalay, Tim Lämmermann, Andrew J Macpherson, Stephanie Christine Ganal-Vonarburg, Rolf Backofen, Daniel Erny, Marco Prinz, Thomas Blank
Gut microbiota drives age-related oxidative stress and mitochondrial damage in microglia via the metabolite N 6 -carboxymethyllysine. Nature neuroscience 25 (3) (2022)
Dominique Batista, Van Dinh Tran, Florian Heyl, Rolf Backofen
RNAProt: an efficient and feature-rich RNA binding protein binding site predictor. GigaScience 10 (8) (2022)
Dominika Grzejda, Jana Mach, Johanna Aurelia Schweizer, Barbara Hummel, Andrew Mischa Rezansoff, Florian Eggenhofer, Amol Panhale, Maria-Eleni Lalioti, Nina Cabezas Wallscheid, Rolf Backofen, Johannes Felsenberg, Valérie Hilgers
The long noncoding RNA mimi scaffolds neuronal granules to maintain nervous system maturity. Science advances 8 (39) (2022)
Joachim Wolff, Rolf Backofen, Bjoern Andreas Gruening
Loop detection using Hi-C data with HiCExplorer. GigaScience 11 (2022)
Simon A Bray, Tim Dudgeon, Rachael E Skyner, Rolf Backofen, Bjoern Andreas Gruening, Frank von Delft
Galaxy workflows for fragment-based virtual screening: a case study on the SARS-CoV-2 main protease. Journal of cheminformatics 14 (1) (2022)
Thomas Clapes, Aikaterini Polyzou, Pia Prater, null Sagar, Antonio Morales-Hernández, Mariana Galvão Ferrarini, Natalie Kehrer, Stylianos Lefkopoulos, Veronica Bergo, Barbara Hummel, Nadine Obier, Daniel Maticzka, Anne Bridgeman, Josip Stefan Herman, Ibrahim Ilik, Lhéanna Klaeylé, Jan Rehwinkel, Shannon McKinney-Freeman, Rolf Backofen, Asifa Akhtar, Nina Cabezas-Wallscheid, Ritwick Sawarkar, Rita Rebollo, Dominic Grün, Eirini Trompouki
Publisher Correction: Chemotherapy-induced transposable elements activate MDA5 to enhance haematopoietic regeneration. Nature cell biology (2021)
Martin Raden, Thomas Wallach, Milad Miladi, Yuanyuan Zhai, Christina Krüger, Zoé J Mossmann, Paul Dembny, Rolf Backofen, Seija Lehnardt
Structure-aware machine learning identifies microRNAs operating as Toll-like receptor 7/8 ligands. RNA biology (2021)
Omer S Alkhnbashi, Alexander Mitrofanov, Robson Bonidia, Martin Raden, Van Dinh Tran, Florian Eggenhofer, Shiraz A Shah, Ekrem Öztürk, Victor A Padilha, Danilo S Sanches, André C P L F de Carvalho, Rolf Backofen
CRISPRloci: comprehensive and accurate annotation of CRISPR-Cas systems. Nucleic acids research 49 (W1) (2021)
Thomas Clapes, Aikaterini Polyzou, Pia Prater, null Sagar, Antonio Morales-Hernández, Mariana Galvão Ferrarini, Natalie Kehrer, Stylianos Lefkopoulos, Veronica Bergo, Barbara Hummel, Nadine Obier, Daniel Maticzka, Anne Bridgeman, Josip Stefan Herman, Ibrahim Ilik, Lhéanna Klaeylé, Jan Rehwinkel, Shannon McKinney-Freeman, Rolf Backofen, Asifa Akhtar, Nina Cabezas-Wallscheid, Ritwick Sawarkar, Rita Rebollo, Dominic Grün, Eirini Trompouki
Chemotherapy-induced transposable elements activate MDA5 to enhance haematopoietic regeneration. Nature cell biology 23 (7) (2021)
Anzhela Migur, Florian Heyl, Janina Fuss, Afshan Srikumar, Bruno Huettel, Claudia Steglich, Prakash Syama Sundar Jogadhenu, Richard Reinhardt, Rolf Backofen, George W Owttrim, Wolfgang R Hess
The temperature-regulated DEAD-box RNA helicase CrhR interactome: Autoregulation and photosynthesis-related transcripts. Journal of experimental botany (2021)
Milad Miladi, Martin Raden, Sebastian Will, Rolf Backofen
Fast and accurate structure probability estimation for simultaneous alignment and folding of RNAs with Markov chains. Algorithms for molecular biology : AMB 15 (1) (2020)
Elisa Venturini, Sarah L Svensson, Sandra Maaß, Rick Gelhausen, Florian Eggenhofer, Lei Li, Amy K Cain, Julian Parkhill, Dörte Becher, Rolf Backofen, Lars Barquist, Cynthia Mira Sharma, Alexander J Westermann, Jörg Vogel
A global data-driven census of Salmonella small proteins and their potential functions in bacterial virulence. microLife 1 (1) (2020)
Michael Uhl, Van Dinh Tran, Rolf Backofen
Improving CLIP-seq data analysis by incorporating transcript information. BMC genomics 21 (1) (2020)
Yogita Sharma, Milad Miladi, Sandeep Dukare, Karine Boulay, Maiwen Caudron-Herger, Matthias Groß, Rolf Backofen, Sven Diederichs
A pan-cancer analysis of synonymous mutations. Nature communications 10 (1) (2019)
Shiraz A Shah, Omer S Alkhnbashi, Juliane Behler, Wenyuan Han, Qunxin She, Wolfgang R Hess, Roger A Garrett, Rolf Backofen
Comprehensive search for accessory proteins encoded with archaeal and bacterial type III CRISPR-cas gene cassettes reveals 39 new cas gene families. RNA biology 16 (4) (2018)
Yajia Zhang, Sethuramasundaram Pitchiaya, Marcin Cieślik, Yashar S Niknafs, Jean C-Y Tien, Yasuyuki Hosono, Matthew K Iyer, Sahr Yazdani, Shruthi Subramaniam, Sudhanshu K Shukla, Xia Jiang, Lisha Wang, Tzu-Ying Liu, Dominique Batista, Alexander R Gawronski, Yuanyuan Qiao, Lanbo Xiao, Saravana M Dhanasekaran, Kristin M Juckette, Lakshmi P Kunju, Xuhong Cao, Utsav Patel, Mona Batish, Girish C Shukla, Michelle T Paulsen, Mats Ljungman, Hui Jiang, Rohit Mehra, Rolf Backofen, Cenk S Sahinalp, Susan M Freier, Andrew T Watt, Shuling Guo, John T Wei, Felix Y Feng, Rohit Malik, Arul M Chinnaiyan
Analysis of the androgen receptor-regulated lncRNA landscape identifies a role for ARLNC1 in prostate cancer progression. Nature genetics 50 (6) (2018)
Shengwei Hou, Manuel Brenes-Álvarez, Viktoria Reimann, Omer S Alkhnbashi, Rolf Backofen, Alicia M Muro-Pastor, Wolfgang R Hess
CRISPR-Cas systems in multicellular cyanobacteria. RNA biology 16 (4) (2018)
Daniel Maticzka, Ibrahim Avsar Ilik, Tugce Aktas, Rolf Backofen, Asifa Akhtar
uvCLAP is a fast and non-radioactive method to identify in vivo targets of RNA-binding proteins. Nature communications 9 (1) (2018)
Lisa Nickel, Andrea Ulbricht, Omer S Alkhnbashi, Konrad U Förstner, Liam Cassidy, Katrin Weidenbach, Rolf Backofen, Ruth Anne Schmitz
Cross-cleavage activity of Cas6b in crRNA processing of two different CRISPR-Cas systems in Methanosarcina mazei Gö1. RNA biology 16 (4) (2018)
Frederick Rehfeld, Daniel Maticzka, Sabine Grosser, Pina Knauff, Murat Eravci, Imre Vida, Rolf Backofen, F Gregory Wulczyn
The RNA-binding protein ARPP21 controls dendritic branching by functionally opposing the miRNA it hosts. Nature communications 9 (1) (2018)
Ralf Gilsbach, Martin Schwaderer, Sebastian Preissl, Björn A Grüning, David Kranzhöfer, Pedro Schneider, Thomas G Nührenberg, Sonia Mulero-Navarro, Dieter Weichenhan, Christian Braun, Martina Dreßen, Adam R Jacobs, Harald Lahm, Torsten Doenst, Rolf Backofen, Markus Krane, Bruce D Gelb, Lutz Hein
Distinct epigenetic programs regulate cardiac myocyte development and disease in the human heart in vivo. Nature communications 9 (1) (2018)
Fabrizio Costa, Dominic Grün, Rolf Backofen
GraphDDP: a graph-embedding approach to detect differentiation pathways in single-cell-data using prior class knowledge. Nature communications 9 (1) (2018)
Laura V Glaser, Simone Rieger, Sybille Thumann, Sophie Beer, Cornelia Kuklik-Roos, Dietmar E Martin, Kerstin C Maier, Marie L Harth-Hertle, Bjoern Andreas Gruening, Rolf Backofen, Stefan Krebs, Helmut Blum, Ralf Zimmer, Florian Erhard, Bettina Kempkes
EBF1 binds to EBNA2 and promotes the assembly of EBNA2 chromatin complexes in B cells. PLoS pathogens 13 (10) (2017)

Rolf Backofen.css-eqlu8i{font-size:small;padding-left:4px;}

Publication Activity (10 Years)

Top Topics

Top Venues

Rolf Backofen